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Defining Microbiota and Microbiome

Author: John Deaton, Ph.D.

Many people now have heard the term “probiotics” and understand that they are beneficial for digestive, immune and overall health. Probiotics, as supplements and in yogurt, have been consumed knowledgeably for these general health benefits.

Two newer (to consumer) terms have now been showing up in health and mass media, “microbiota” and “microbiome.” And they are often misunderstood, and used incorrectly. We feel it is important to clarify what these mean, so that when we report about new strains of probiotics – and how they interact in the microbiota and potentially affect the microbiome – it will be more easily understood.

Microbiota refers to a bio-ecological community (that’s city-like) composed of multiple symbiotic, commensal and even pathogenic microorganisms. It’s like any community, with members that work to keep it whole, and of course, a “bad element;” but if, like healthy communities, that bad element can be kept in check, the community can function pretty well, even under duress. Commensal bacteria are part of the normal flora community in the oral cavity, and a commensal bacterium benefits from another without harming it.

The human microbiota is indeed like a city – it contains trillions of bacteria; it also contains fungi, viruses, protists (single celled organisms) and archaea (microbes without a cell nucleus or any membrane-bound organelles). The microbiota, in large part, resides in the gut.

The microbiota is impacted by diet and other lifestyle factors that the individual host practices. And, like fingerprints, the composition of microbiota is individualized, no two are exactly alike. Some people have fewer elements in their communities than others.

Meanwhile, the microbiome refers to the genes contained in the organisms comprising the microbiota – and these genes are also being studied in the same manner as the human genome. Researchers Grice and Segre in their published article “The Human Microbiome: Our Second Genome” (Annu Rev Genomics Hum Genet June 6, 2013), write, “Characterization and analysis of the human microbiome have been greatly catalyzed by advances in genomic technologies.”

Research in the past five years has suggested that there is an association between number of genes in the microbiome and diet. Several studies also associate a higher microbiome count with healthy weight range, less inflammation, lower risk of diabetes and a more effectively functioning immune system than individuals with a lower gene count. And typically, these studies have found that those with a less dense microbiome also regularly consumed red meats and more fat; while those with higher bacterial gene count tended to have a more plant-based diet.

The microbiota inside everyone is a living community and is impacted by the host’s diet (among other lifestyle factors), and there are certain foods that help populate and promote a healthy gut community. Overall, research has shown that glucosinolates found in cruciferous vegetables can help ensure certain pathogens are not allowed into the enclave, and insoluble fibers such as inulin ferment in the colon, creating new good neighbors. Beans are excellent as well, as they also serve to feed the community.

Not everyone can eat beans, or fermented foods, so this is where probiotic and enzyme supplements become valuable municipal employees for the microbiota community. A healthy microbiota is one of diversity, and probiotic (and prebiotic) supplements greatly enhance the composition and functionality of that community, while enzyme supplements help facilitate smooth and more effective digestion, which in turn, supports the community.

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About The Expert

John Deaton, Ph.D.

Vice President of Science & Technology, Deerland Enzymes & Probiotics

Dr. John Deaton is vice president of technology at Deerland Enzymes, with more than 18 years experience working with proteins and enzymes. He holds a PhD in biochemistry from Texas A&M University, with post-graduate studies in microbiology, biophysics and cancer research. He has two papers published in the Proceedings of the National Academy of Sciences (PNAS) and is a six-year member of the Association of Official Analytical Chemists (AOAC), with three years served on the committee of microbiology.